In simulations of biomolecular systems performance is critical, and parallel computing is an essential enabling technology. One million force-field evaluations are required to obtain a single nanosecond of simulated time. For large systems this may require a month or more of run time. In addition, the state of the art progresses at a steady pace, producing new and better integrators, long-range electrostatic methods, and simulation protocols. Experimenting with alternate novel strategies, and reusing new libraries with faster algorithms without having to implement an entirely new program present additional challenges. We have addressed these challenges in the program NAMD2, creating a software system which obtains excellent parallel speedups and serial performance on an increasing variety of distributed memory platforms while being flexible enough to incorporate new algorithms and externally developed packages. Owing to the Converse parallel runtime system, NAMD2 can even interoperate at the library level with parallel packages written in a variety of parallel languages and paradigms.

TextRef

Robert Brunner and Laxmikant Kale and James Phillips, "Flexibility and
Interoperability in a Parallel Molecular Dynamics Code", Object Oriented
Methods for Inter-operable Scientific and Engineering Computing, SIAM,
October 1998, pp. 80--89